Multi-omic Directed Networks Describe Features of Gene Regulation in Aged Brains and Expand the Set of Genes Driving Cognitive Decline

Religious Orders Study and Rush Memory and Aging Project

(2018) David A. Bennett et al.   JOURNAL OF ALZHEIMERS DISEASE

Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals

(2018) James J. Lee et al.   NATURE GENETICS

A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer’s disease

(2018) Sara Mostafavi et al.   NATURE NEUROSCIENCE

Genome-wide association meta-analysis of 78,308 individuals identifies new loci and genes influencing human intelligence

(2017) Suzanne Sniekers et al.   NATURE GENETICS

An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome

(2017) Bernard Ng et al.   NATURE NEUROSCIENCE

Locus-specific histone deacetylation using a synthetic CRISPR-Cas9-based HDAC

(2017) Deborah Y. Kwon et al.   Nature Communications

Why has therapy development for dementia failed in the last two decades?

(2016) Serge Gauthier et al.   Alzheimers & Dementia

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

(2016) Lu Chen et al.   CELL

Editing DNA Methylation in the Mammalian Genome

(2016) X. Shawn Liu et al.   CELL

Accelerating Medicines Partnership: Alzheimer’s Disease (AMP-AD) Knowledge Portal Aids Alzheimer’s Drug Discovery through Open Data Sharing

(2016) Richard J. Hodes et al.   EXPERT OPINION ON THERAPEUTIC TARGETS

GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments

(2016) Ivan Yevshin et al.   NUCLEIC ACIDS RESEARCH

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Fast and efficient QTL mapper for thousands of molecular phenotypes

(2015) Halit Ongen et al.   BIOINFORMATICS

Bayesian Network Reconstruction Using Systems Genetics Data: Comparison of MCMC Methods

(2015) Shinya Tasaki et al.   GENETICS

TRIOloss of function is associated with mild intellectual disability and affects dendritic branching and synapse function

(2015) Wei Ba et al.   HUMAN MOLECULAR GENETICS

What are super-enhancers?

(2015) Sebastian Pott et al.   NATURE GENETICS

A New Initiative on Precision Medicine

(2015) Francis S. Collins et al.   NEW ENGLAND JOURNAL OF MEDICINE

dbSUPER: a database of super-enhancers in mouse and human genome

(2015) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Bayesian Network Reconstruction Using Systems Genetics Data: Comparison of MCMC Methods

(2015) Shinya Tasaki et al.   GENETICS

Epigenetic Priming of Memory Updating during Reconsolidation to Attenuate Remote Fear Memories

(2014) Johannes Gräff et al.   CELL

Neural Cell Adhesion Molecule NrCAM Regulates Semaphorin 3F-Induced Dendritic Spine Remodeling

(2014) G. P. Demyanenko et al.   JOURNAL OF NEUROSCIENCE

Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci

(2014) Philip L De Jager et al.   NATURE NEUROSCIENCE

Alzheimer’s disease drug-development pipeline: few candidates, frequent failures

(2014) Jeffrey L Cummings et al.   Alzheimers Research & Therapy

Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels

(2014) Nicholas E. Banovich et al.   PLoS Genetics

Much of late life cognitive decline is not due to common neurodegenerative pathologies

(2013) Patricia A. Boyle et al.   ANNALS OF NEUROLOGY

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease

(2013) Bin Zhang et al.   CELL

Overview and Findings from the Religious Orders Study

(2013) David A. Bennett et al.   Current Alzheimer Research

Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease

(2013) Jean-Charles Lambert et al.   NATURE GENETICS

Passive and active DNA methylation and the interplay with genetic variation in gene regulation

(2013) Maria Gutierrez-Arcelus et al.   eLife

Relation of neuropathology to cognition in persons without cognitive impairment

(2012) David A. Bennett et al.   ANNALS OF NEUROLOGY

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

Cognitive impairment, decline and fluctuations in older community-dwelling subjects with Lewy bodies

(2012) J. A. Schneider et al.   BRAIN

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

Statistical colocalization of monocyte gene expression and genetic risk variants for type 1 diabetes

(2012) Chris Wallace et al.   HUMAN MOLECULAR GENETICS

Neurodegeneration-associated TDP-43 Interacts with Fragile X Mental Retardation Protein (FMRP)/Staufen (STAU1) and Regulates SIRT1 Expression in Neuronal Cells

(2012) Zhipeng Yu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Mutations in DNMT1 cause hereditary sensory neuropathy with dementia and hearing loss

(2011) Christopher J Klein et al.   NATURE GENETICS

A genome-wide scan for common variants affecting the rate of age-related cognitive decline

(2011) Philip L. De Jager et al.   NEUROBIOLOGY OF AGING

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis

(2010) Pan Du et al.   BMC BIOINFORMATICS

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

(2010) Oliver Stegle et al.   PLoS Computational Biology

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Improving the structure MCMC sampler for Bayesian networks by introducing a new edge reversal move

(2008) Marco Grzegorczyk et al.   MACHINE LEARNING

Staufen1 Regulation of Protein Synthesis-Dependent Long-Term Potentiation and Synaptic Function in Hippocampal Pyramidal Cells

(2008) G. Lebeau et al.   MOLECULAR AND CELLULAR BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY